[gmx-users] Genion error

‪Mohammad Roostaie‬ ‪ mohammad.r0325 at yahoo.com
Tue May 30 18:00:54 CEST 2017

Thank you very much Justin. It is good now.

      From: Justin Lemkul <jalemkul at vt.edu>
 To: gmx-users at gromacs.org 
 Sent: Monday, 29 May 2017, 23:40:06
 Subject: Re: [gmx-users] Genion error

On 5/29/17 4:35 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Thank you Justin. Here is the link to access the topology file:https://www.dropbox.com/sh/x58tzpmg0vzkbtg/AADH_efF_s8jKx4OaHN8a7IPa?dl=0
> By the way, I do not know about your advice. Can you please give me the link?

It's somewhere in the archive.  Run the topology through dos2unix and always 
make sure to use a plain text editor.  See if that works.


> Kind regards,Mohammad
>        From: Justin Lemkul <jalemkul at vt.edu>
>  To: gmx-users at gromacs.org
>  Sent: Monday, 29 May 2017, 0:21:10
>  Subject: Re: [gmx-users] Genion error
> On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
>> Hi All, when I wanted to add ions to the system, I got this error:
>> Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section of file 'gr.top'For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
>> However, there is 'SOL' molecule type in the [ molecules ] section of the topology file. Can you please help me to solve this problem?
> Upload your topology to a file-sharing service and provide the URL to access it.
>    There's no way to know what's going on (and I recall giving some previous
> advice about line endings - have you checked this?)
> -Justin


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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